GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

• Complete API documentation:docs.genebe.net/docs/api/overview/

• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

• Python client for pandas:pypi.org/project/genebe/

• Java CLI for VCF files:github.com/pstawinski/genebe-cli

• All tools documented at:docs.genebe.net

API Request Examples for Variant: 1-54999325-G-A (hg38)

Bash / cURL Example

bash

curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=54999325&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

JSON Response (pretty-printed):

json

{
  "variants": [
    {
      "chr": "1",
      "pos": 54999325,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_057176.3",
      "consequences": [
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BSND",
          "gene_hgnc_id": 16512,
          "hgvs_c": "c.139G>A",
          "hgvs_p": "p.Gly47Arg",
          "transcript": "NM_057176.3",
          "protein_id": "NP_476517.1",
          "transcript_support_level": null,
          "aa_start": 47,
          "aa_end": null,
          "aa_length": 320,
          "cds_start": 139,
          "cds_end": null,
          "cds_length": 963,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000651561.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_057176.3"
        },
        {
          "aa_ref": "G",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BSND",
          "gene_hgnc_id": 16512,
          "hgvs_c": "c.139G>A",
          "hgvs_p": "p.Gly47Arg",
          "transcript": "ENST00000651561.1",
          "protein_id": "ENSP00000498282.1",
          "transcript_support_level": null,
          "aa_start": 47,
          "aa_end": null,
          "aa_length": 320,
          "cds_start": 139,
          "cds_end": null,
          "cds_length": 963,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_057176.3",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000651561.1"
        }
      ],
      "gene_symbol": "BSND",
      "gene_hgnc_id": 16512,
      "dbsnp": "rs74315289",
      "frequency_reference_population": 0.0001897232,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 306,
      "gnomad_exomes_af": 0.000193742,
      "gnomad_genomes_af": 0.000151143,
      "gnomad_exomes_ac": 283,
      "gnomad_genomes_ac": 23,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.6239520907402039,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.495,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.9738,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.11,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 3.613,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 14,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PS3,PM1,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 14,
          "benign_score": 0,
          "pathogenic_score": 14,
          "criteria": [
            "PS3",
            "PM1",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_057176.3",
          "gene_symbol": "BSND",
          "hgnc_id": 16512,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.139G>A",
          "hgvs_p": "p.Gly47Arg"
        }
      ],
      "clinvar_disease": " autosomal recessive,BSND-related disorder,Bartter disease type 4A,Bartter syndrome,Bartter syndrome type 4,Hearing loss,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:11 LP:1",
      "phenotype_combined": "Bartter disease type 4A|not provided|Bartter syndrome|BSND-related disorder|Bartter syndrome type 4|Hearing loss, autosomal recessive",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}